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Masi A, Capobianco A, Bobrowski K, Peluso A, Chatgilialoglu C. Hydroxyl Radical vs. One-Electron Oxidation Reactivities in an Alternating GC Double-Stranded Oligonucleotide: A New Type Electron Hole Stabilization. Biomolecules 2023; 13:1493. [PMID: 37892175 PMCID: PMC10605094 DOI: 10.3390/biom13101493] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/30/2023] [Accepted: 10/04/2023] [Indexed: 10/29/2023] Open
Abstract
We examined the reaction of hydroxyl radicals (HO•) and sulfate radical anions (SO4•-), which is generated by ionizing radiation in aqueous solutions under anoxic conditions, with an alternating GC doubled-stranded oligodeoxynucleotide (ds-ODN), i.e., the palindromic 5'-d(GCGCGC)-3'. In particular, the optical spectra of the intermediate species and associated kinetic data in the range of ns to ms were obtained via pulse radiolysis. Computational studies by means of density functional theory (DFT) for structural and time-dependent DFT for spectroscopic features were performed on 5'-d(GCGC)-3'. Comprehensively, our results suggest the addition of HO• to the G:C pair moiety, affording the [8-HO-G:C]• detectable adduct. The previous reported spectra of one-electron oxidation of a variety of ds-ODN were assigned to [G(-H+):C]• after deprotonation. Regarding 5'-d(GCGCGC)-3' ds-ODN, the spectrum at 800 ns has a completely different spectral shape and kinetic behavior. By means of calculations, we assigned the species to [G:C/C:G]•+, in which the electron hole is predicted to be delocalized on the two stacked base pairs. This transient species was further hydrated to afford the [8-HO-G:C]• detectable adduct. These remarkable findings suggest that the double-stranded alternating GC sequences allow for a new type of electron hole stabilization via delocalization over the whole sequence or part of it.
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Affiliation(s)
- Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Krzysztof Bobrowski
- Centre of Radiation Research and Technology, Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland;
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, 84084 Fisciano, Italy; (A.C.); (A.P.)
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, 40129 Bologna, Italy;
- Center for Advanced Technologies, Adam Mickiewicz University, 61-614 Poznań, Poland
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2
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Landi A, Capobianco A, Peluso A. The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study. Molecules 2021; 26:5497. [PMID: 34576968 PMCID: PMC8465834 DOI: 10.3390/molecules26185497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800-1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.
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Affiliation(s)
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, 132, I-84084 Fisciano, SA, Italy; (A.L.); (A.P.)
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3
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The Dynamics of Hole Transfer in DNA. Molecules 2019; 24:molecules24224044. [PMID: 31703470 PMCID: PMC6891780 DOI: 10.3390/molecules24224044] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/31/2019] [Accepted: 11/02/2019] [Indexed: 11/21/2022] Open
Abstract
High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.
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Capobianco A, Velardo A, Peluso A. Single-Stranded DNA Oligonucleotides Retain Rise Coordinates Characteristic of Double Helices. J Phys Chem B 2018; 122:7978-7989. [PMID: 30070843 DOI: 10.1021/acs.jpcb.8b04542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The structures of single-stranded DNA oligonucleotides from dimeric to hexameric sequences have been thoroughly investigated. Computations performed at the density functional level of theory including dispersion forces and solvation show that single-stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates amounting up to 3.3 Å. Previous results, suggesting that single strands should be shorter than double helices, largely originated from the incompleteness of the adopted basis set. Although sensible deviations with respect to standard B-DNA are predicted, computations indicate that sequences rich in stacked adenines are the most ordered ones, favoring the B-DNA pattern and inducing regular arrangements also on flanking nucleobases. Several structural properties of double helices rich in adenine are indeed already reflected by the corresponding single strands.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
| | - Amalia Velardo
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia "A. Zambelli" , Università di Salerno , Via Giovanni Paolo II , I-84084 Fisciano (SA) , Italy
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5
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Capobianco A, Landi A, Peluso A. Modeling DNA oxidation in water. Phys Chem Chem Phys 2018; 19:13571-13578. [PMID: 28513687 DOI: 10.1039/c7cp02029e] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia "Adolfo Zambelli", Università di Salerno, I-84084 Fisciano (SA), Italy.
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Landi A, Borrelli R, Capobianco A, Velardo A, Peluso A. Hole Hopping Rates in Organic Semiconductors: A Second-Order Cumulant Approach. J Chem Theory Comput 2018; 14:1594-1601. [DOI: 10.1021/acs.jctc.7b00858] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alessandro Landi
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano (SA), Italy
| | - Raffaele Borrelli
- Department of Agricultural, Forestry and Food Science, University of Torino, I-10195 Grugliasco, Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano (SA), Italy
| | - Amalia Velardo
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano (SA), Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università di Salerno, Via Giovanni Paolo II, I-84084 Fisciano (SA), Italy
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Capaccio V, Capobianco A, Stanzione A, Pierri G, Tedesco C, Di Mola A, Massa A, Palombi L. Organocatalytic Heterocyclization Driven by Dynamic Kinetic Resolution: Enantioselective Access to Multi-heteroatomic Cyclic Structures Mediated by Cinchona Alkaloid-based Catalysts. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700472] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- V. Capaccio
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - A. Capobianco
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - A. Stanzione
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - G. Pierri
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - C. Tedesco
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - A. Di Mola
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - A. Massa
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
| | - L. Palombi
- Dipartimento di Chimica e Biologia; Università degli studi di Salerno; Via Giovanni Paolo II, I- 84084 Fisciano (SA) Italy
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Centore R, Manfredi C, Capobianco A, Volino S, Ferrara MV, Carella A, Fusco S, Peluso A. Solid State Separation and Isolation of Tautomers of Fused-Ring Triazolotriazoles. J Org Chem 2017; 82:5155-5161. [PMID: 28452478 DOI: 10.1021/acs.joc.7b00380] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fine control of the tautomeric forms of [1,2,4]triazolo[3,2-c][1,2,4]triazole derivatives in acidic conditions has been achieved by acting on the electronic character of the substituent at position 7 of the heterobicycle and on the counterion. Strong electron releasing or electron withdrawing substituents lead almost exclusively to a single tautomeric form, the 1H-3H or the 2H-3H, respectively. In the case of the phenol substituent, both tautomeric forms are present in comparable amount in solution; the two tautomers can also be selectively precipitated in different crystalline salts using suitable counterions.
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Affiliation(s)
- Roberto Centore
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Carla Manfredi
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Amedeo Capobianco
- Department of Chemistry and Biology, University of Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
| | - Sabato Volino
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Maria Vittoria Ferrara
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Antonio Carella
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Sandra Fusco
- Department of Chemical Sciences, University of Naples Federico II , Via Cintia, I-80126 Naples, Italy
| | - Andrea Peluso
- Department of Chemistry and Biology, University of Salerno , Via Giovanni Paolo II, 132, I-84084 Fisciano, Salerno, Italy
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9
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Capobianco A, Borrelli R, Landi A, Velardo A, Peluso A. Absorption Band Shapes of a Push–Pull Dye Approaching the Cyanine Limit: A Challenging Case for First Principle Calculations. J Phys Chem A 2016; 120:5581-9. [DOI: 10.1021/acs.jpca.6b05220] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Amedeo Capobianco
- Dipartimento
di Chimica e Biologia, Università di Salerno, Via G. Paolo
II, I-84084 Fisciano (SA), Italy
| | - Raffaele Borrelli
- Dipartimento
di Scienze Agrarie, Forestali e Alimentari, Università di Torino, Largo Paolo Braccini, 2, I-10095 Grugliasco (TO), Italy
| | - Alessandro Landi
- Dipartimento
di Chimica e Biologia, Università di Salerno, Via G. Paolo
II, I-84084 Fisciano (SA), Italy
| | - Amalia Velardo
- Dipartimento
di Chimica e Biologia, Università di Salerno, Via G. Paolo
II, I-84084 Fisciano (SA), Italy
| | - Andrea Peluso
- Dipartimento
di Chimica e Biologia, Università di Salerno, Via G. Paolo
II, I-84084 Fisciano (SA), Italy
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10
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Capobianco A, Caruso T, Peluso A. Hole delocalization over adenine tracts in single stranded DNA oligonucleotides. Phys Chem Chem Phys 2016; 17:4750-6. [PMID: 25589467 DOI: 10.1039/c4cp04282d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Adiabatic ionization energies of single stranded DNA oligonucleotides containing adenine tracts of different sizes have been computed at the DFT level and compared with the oxidation potentials determined by differential pulse voltammetry. Geometry optimizations have been performed at the full quantum mechanical level, including the sugar phosphate backbone and solvent effects. The observed progressive lowering of the ionization energy upon increasing the number of consecutive adenines is well predicted, the computed ionization potential shifts being in very good agreement with the experimental outcomes, both by using pure and hybrid functionals. The spin density of the oligonucleotide radical cations is distributed almost over the whole adenine tract, forming delocalized polarons.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia, Università di Salerno, I-84084 Fisciano, SA, Italy.
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11
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12
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Capobianco A, Caruso T, D'Ursi AM, Fusco S, Masi A, Scrima M, Chatgilialoglu C, Peluso A. Delocalized hole domains in Guanine-rich DNA oligonucleotides. J Phys Chem B 2015; 119:5462-6. [PMID: 25839102 DOI: 10.1021/acs.jpcb.5b02940] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Differential pulse voltammetries of guanine-rich single- and double-stranded oligonucleotides containing up to six consecutive guanines are reported. The observed progressive lowering of the first voltammetric peak potential as the number of adjacent guanines increases unambiguously points toward the establishment of delocalized hole domains; the hole stabilization energy is ca. 0.1 eV per GG step, significantly lower than that observed for AA steps.
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Affiliation(s)
| | | | | | | | - Annalisa Masi
- §Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy
| | | | - Chryssostomos Chatgilialoglu
- §Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, I-40129 Bologna, Italy.,∥National Center for Scientific Research "Demokritos", Institute of Nanoscience and Nanotechnology, 15341 Agia Paraskevi, Athens, Greece
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Capobianco A, Caruso T, Fusco S, Terzidis MA, Masi A, Chatgilialoglu C, Peluso A. The association constant of 5',8-cyclo-2'-deoxyguanosine with cytidine. Front Chem 2015; 3:22. [PMID: 25870853 PMCID: PMC4376000 DOI: 10.3389/fchem.2015.00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Accepted: 03/06/2015] [Indexed: 01/11/2023] Open
Abstract
The association of 5′,8-cyclo-2′-deoxyguanosine (cdG), a DNA tandem lesion, with its complementary base cytosine has been studied by voltammetry and NMR in chloroform, using properly silylated derivatives of the two nucleobases for increasing their solubilities. Both voltammetric data and NMR titrations indicated that the Watson-Crick complex of cytidine with cdG is weaker than that with guanosine, the difference being approximately of one order of magnitude between the two association constants.
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Affiliation(s)
- Amedeo Capobianco
- Dipartimento di Chimica e Biologia, Università di Salerno Fisciano, Salerno, Italy
| | - Tonino Caruso
- Dipartimento di Chimica e Biologia, Università di Salerno Fisciano, Salerno, Italy
| | - Sandra Fusco
- Dipartimento di Chimica e Biologia, Università di Salerno Fisciano, Salerno, Italy
| | - Michael A Terzidis
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy
| | - Annalisa Masi
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche Bologna, Italy ; Institute of Nanoscience and Nanotechnology, National Center for Scientific Research "Demokritos," Athens, Greece
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia, Università di Salerno Fisciano, Salerno, Italy
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Borrelli R, Capobianco A, Landi A, Peluso A. Vibronic couplings and coherent electron transfer in bridged systems. Phys Chem Chem Phys 2015; 17:30937-45. [DOI: 10.1039/c5cp01190f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A computational strategy to analyze the dynamics of coherent electron transfer processes in bridged systems, involving three or more electronic states, is presented.
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Affiliation(s)
- Raffaele Borrelli
- Department of Agricultural
- Forestry and Food Science
- University of Torino
- I-10095 Grugliasco
- Italy
| | - Amedeo Capobianco
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
| | - Alessandro Landi
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
| | - Andrea Peluso
- Dipartimento di Chimica e Biologia
- Università di Salerno
- I-84084 Fisciano (SA)
- Italy
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15
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Capobianco A, Peluso A. The oxidization potential of AA steps in single strand DNA oligomers. RSC Adv 2014. [DOI: 10.1039/c4ra09270h] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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